Variant report

Variant	rs62106867
Chromosome Location	chr19:40324476-40324477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr19:40322859-40325426	GM12878	blood:	n/a	n/a
2	SIN3A	chr19:40323786-40325203	H1-hESC	embryonic stem cell:	n/a	chr19:40324858-40324867
3	ELF1	chr19:40323743-40325117	GM12878	blood:	n/a	chr19:40323990-40324002
4	USF2	chr19:40324130-40325172	H1-hESC	embryonic stem cell:	n/a	chr19:40324856-40324867 chr19:40324851-40324872 chr19:40324858-40324867 chr19:40324857-40324866 chr19:40324855-40324868 chr19:40324520-40324536 chr19:40324857-40324866 chr19:40324528-40324544
5	EP300	chr19:40324038-40325677	A549	lung:	n/a	n/a
6	RCOR1	chr19:40324055-40325041	K562	blood:	n/a	n/a
7	ELF1	chr19:40324020-40325132	MCF-7	breast:	n/a	n/a
8	POU2F2	chr19:40324029-40325143	GM12891	blood:	n/a	chr19:40324229-40324241 chr19:40324843-40324855
9	EP300	chr19:40324011-40324921	T-47D	breast:	n/a	n/a
10	TBL1XR1	chr19:40324134-40325221	K562	blood:	n/a	n/a
11	MYC	chr19:40324269-40324989	MCF10A-Er-Src	breast:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324857-40324866 chr19:40324812-40324821
12	YY1	chr19:40324327-40325007	GM12891	blood:	n/a	chr19:40324774-40324796 chr19:40324786-40324796 chr19:40324891-40324899 chr19:40324878-40324900 chr19:40324785-40324793
13	POLR2A	chr19:40323851-40325236	H1-neurons	neurons:	n/a	n/a
14	USF1	chr19:40324061-40324541	H1-hESC	embryonic stem cell:	n/a	chr19:40324085-40324101 chr19:40324520-40324536
15	USF1	chr19:40323916-40325224	ECC-1	luminal epithelium:	n/a	chr19:40324851-40324872 chr19:40324858-40324867 chr19:40324857-40324866 chr19:40324085-40324101 chr19:40324855-40324868 chr19:40324520-40324536 chr19:40324857-40324866 chr19:40324528-40324544
16	SIN3AK20	chr19:40324044-40324932	PFSK-1	brain:	n/a	n/a
17	MAZ	chr19:40324066-40325043	Hela-S3	cervix:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
18	YY1	chr19:40324166-40325114	SK-N-SH	brain:	n/a	chr19:40324774-40324796 chr19:40324786-40324796 chr19:40324269-40324283 chr19:40324891-40324899 chr19:40324878-40324900 chr19:40324785-40324793
19	ATF3	chr19:40324107-40325326	A549	lung:	n/a	chr19:40324649-40324658 chr19:40324857-40324866
20	MAX	chr19:40323793-40325208	ECC-1	luminal epithelium:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
21	STAT3	chr19:40324416-40324616	MCF10A-Er-Src	breast:	n/a	chr19:40324492-40324501 chr19:40324493-40324502 chr19:40324490-40324504
22	ZKSCAN1	chr19:40324316-40325009	Hela-S3	cervix:	n/a	n/a
23	YY1	chr19:40324284-40325040	K562	blood:	n/a	chr19:40324774-40324796 chr19:40324786-40324796 chr19:40324891-40324899 chr19:40324878-40324900 chr19:40324785-40324793
24	POLR2A	chr19:40323486-40325688	GM12878	blood:	n/a	n/a
25	ELF1	chr19:40324039-40325229	A549	lung:	n/a	n/a
26	POLR2A	chr19:40323959-40325154	GM12892	blood:	n/a	n/a
27	MAX	chr19:40324127-40325099	Hela-S3	cervix:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
28	MAX	chr19:40323896-40325337	K562	blood:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
29	POLR2A	chr19:40324081-40325153	GM12891	blood:	n/a	n/a
30	E2F6	chr19:40324475-40324689	K562	blood:	n/a	n/a
31	TAF1	chr19:40324427-40325146	H1-neurons	neurons:	n/a	n/a
32	SIN3AK20	chr19:40324018-40325305	A549	lung:	n/a	n/a
33	WRNIP1	chr19:40324151-40324551	GM12878	blood:	n/a	n/a
34	ZBTB7A	chr19:40323658-40324701	ECC-1	luminal epithelium:	n/a	chr19:40323952-40323960
35	POLR2A	chr19:40324061-40325336	K562	blood:	n/a	n/a
36	POLR2A	chr19:40323939-40325209	U87	brain:	n/a	n/a
37	YY1	chr19:40323868-40325090	SK-N-SH_RA	brain:	n/a	chr19:40323986-40324000 chr19:40324774-40324796 chr19:40323974-40323993 chr19:40324786-40324796 chr19:40324269-40324283 chr19:40323969-40323991 chr19:40324891-40324899 chr19:40323979-40323991 chr19:40324878-40324900 chr19:40324105-40324114 chr19:40323936-40323947 chr19:40324785-40324793
38	CEBPB	chr19:40324162-40325272	A549	lung:	n/a	chr19:40324353-40324361
39	POLR2A	chr19:40323967-40325128	MCF-7	breast:	n/a	n/a
40	REST	chr19:40324103-40325382	A549	lung:	n/a	chr19:40324393-40324413 chr19:40324106-40324119 chr19:40324521-40324534
41	POLR2A	chr19:40323839-40325238	Hela-S3	cervix:	n/a	n/a
42	ZNF143	chr19:40324235-40325024	Hela-S3	cervix:	n/a	n/a
43	YY1	chr19:40323749-40325188	GM12878	blood:	n/a	chr19:40323986-40324000 chr19:40324774-40324796 chr19:40323974-40323993 chr19:40324786-40324796 chr19:40324269-40324283 chr19:40323969-40323991 chr19:40324891-40324899 chr19:40323979-40323991 chr19:40324878-40324900 chr19:40324105-40324114 chr19:40323936-40323947 chr19:40324785-40324793
44	MAX	chr19:40323904-40325205	H1-hESC	embryonic stem cell:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
45	FOS	chr19:40324154-40324541	K562	blood:	n/a	chr19:40324354-40324363 chr19:40324229-40324238
46	EGR1	chr19:40324325-40325027	K562	blood:	n/a	chr19:40324825-40324839 chr19:40324909-40324918 chr19:40324986-40324995 chr19:40324828-40324841
47	MAZ	chr19:40323889-40325096	GM12878	blood:	n/a	chr19:40324310-40324319 chr19:40324544-40324554 chr19:40324166-40324176 chr19:40324857-40324866 chr19:40324812-40324821
48	TAF1	chr19:40323913-40324867	H1-hESC	embryonic stem cell:	n/a	n/a
49	NR2F2	chr19:40324037-40325337	K562	blood:	n/a	n/a
50	POU2F2	chr19:40324298-40324532	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40323585..40327109-chr19:40328017..40332842,7	MCF-7	breast:
2	chr19:40318662..40321360-chr19:40322185..40325984,6	MCF-7	breast:
3	chr19:40323873..40328898-chr19:40330848..40333267,4	MCF-7	breast:
4	chr19:39926032..39928483-chr19:40324303..40326455,2	MCF-7	breast:
5	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:
6	chr19:39900130..39902222-chr19:40323529..40326104,2	MCF-7	breast:
7	chr19:40323895..40326074-chr19:40326895..40329517,2	MCF-7	breast:
8	chr19:40322842..40325581-chr19:40335629..40338491,6	MCF-7	breast:
9	chr19:40321676..40323398-chr19:40323422..40325295,2	MCF-7	breast:

Variant related genes	Relation type
DYRK1B	TF binding region
ENSG00000105204	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000105193	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10422280	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880094	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880956	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11883249	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980289	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072290	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354800	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810383	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810386	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803297	0.96[ASN][1000 genomes]
rs616650	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619350	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508912	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508913	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718066	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246501	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7248926	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253739	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254914	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258351	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40318000-40331800	Strong transcription	HepG2	liver
2	chr19:40322600-40325600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:40323000-40325000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr19:40323200-40325000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:40323400-40324800	Active TSS	Fetal Muscle Trunk	muscle
6	chr19:40323400-40325000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:40323400-40325000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:40323400-40325000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr19:40323400-40325000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:40323400-40325000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:40323600-40324600	Active TSS	Right Atrium	heart
12	chr19:40323600-40324800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr19:40323600-40324800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:40323600-40324800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:40323600-40324800	Active TSS	Esophagus	oesophagus
16	chr19:40323600-40324800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr19:40323600-40324800	Active TSS	Ovary	ovary
18	chr19:40323600-40325000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr19:40323600-40325000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:40323600-40325000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:40323600-40325000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:40323600-40325000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:40323600-40325000	Active TSS	Fetal Kidney	kidney
24	chr19:40323600-40325000	Active TSS	Gastric	stomach
25	chr19:40323600-40325000	Active TSS	Hela-S3	cervix
26	chr19:40323600-40325000	Active TSS	NH-A	brain
27	chr19:40323600-40325000	Active TSS	NHDF-Ad	bronchial
28	chr19:40323600-40325400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:40323800-40324600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:40323800-40324800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:40323800-40324800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:40323800-40324800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:40323800-40324800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:40323800-40324800	Active TSS	Aorta	Aorta
35	chr19:40323800-40324800	Active TSS	Placenta	Placenta
36	chr19:40323800-40324800	Active TSS	Placenta Amnion	Placenta Amnion
37	chr19:40323800-40324800	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr19:40323800-40324800	Active TSS	Small Intestine	intestine
39	chr19:40323800-40324800	Active TSS	Stomach Smooth Muscle	stomach
40	chr19:40323800-40324800	Active TSS	NHEK	skin
41	chr19:40323800-40325000	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr19:40323800-40325000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:40323800-40325000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:40323800-40325000	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr19:40323800-40325000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:40323800-40325000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:40323800-40325000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:40323800-40325000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr19:40323800-40325000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:40323800-40325000	Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links